The 27-year-old German delivered a fastest lap of one minute and 13.876 seconds in the final seconds of a rain-hit session to outpace 2008 world champion Hamilton by 0.091 seconds.
It was Rosberg's third successive pole, the team's fourth in a row and the fourth of his career, and it set him up perfectly to attempt to become the first son of a victorious former Monaco winner to triumph on the streets of the Mediterranean principality.
"You know, it's always nice to hear statistics like that," Rosberg junior said.
"But it doesn't change much for tomorrow. Of course, I'm very happy.
"But, in Barcelona, we were struggling such a lot in the race (after starting from pole) and I finished 70 seconds behind the winner.
"We're improving step by step, but there are still a lot of questions remaining. It's still our weakness. But we will make the best of it and who knows."
Hamilton, who has been outpaced by Rosberg in all three practice sessions as well as qualifying, said: "I've been struggling all weekend and my pace has been slacking.
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